Development of a Sequence-Characterized Amplified Region (SCAR) Marker for the Identification of the Korean Garlic Cultivar ‘Hongsan’ Derived from RAPD

Garlic (Allium sativum L.) cultivars in Korea, particularly the widely adaptable ‘Hongsan’, are challenging to identify in processed forms or seedlings due to the plasticity of phenotypic traits such as clove tip greening, which risks mislabeling and infringement of UPOV breeders' rights. This study aimed to develop a stable SCAR marker for ‘Hongsan’-specific identification using RAPD-bulked segregant analysis (BSA). Sixty Operon primers (>60% GC) were screened against ‘Hongsan’ gDNA versus a non-’Hongsan’ BSA pool (‘Daeseo’, ‘Uiseong’, ‘Danyang’, and ‘Namdo’); OPE-01 consistently amplified a unique 1.3 kb band, cloned and sequenced to reveal a 1,272 bp sequence with translocation junction (878+394 bp), 18 bp insertion, and EcoRI site on chromosome 2 (NCBI GCA_030737875.1). SCAR primers SaH191R/SaH513F produced a specific 545 bp amplicon in ‘Hongsan’, clearly distinguishing it from other cultivars and parental lines, confirming paternal origin (9209). This RAPD-to-SCAR marker overcomes reproducibility limitations, enabling authentication in processing (powders, black garlic) irrespective of environmental factors. The cost-effective and rapid assay ensures industry transparency, quality control, and IP protection for Korean garlic production.